Papain: Difference between revisions

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==='''Stefin B'''===

<scene name='Papain/~~Sk_inhibitor_0~~/2'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases-- it binds tightly but reversibly to the papain active site. Stefin inhibitors are characterized by M<sub>r</sub> of about 11,000, no disulfide bonds and no associated carbohydrates.

<scene name='Papain/Stefin_b/1'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases- it binds tightly but reversibly to the papain active site. Stefin inhibitors are characterized by M<sub>r</sub> of about 11,000, no disulfide bonds and no associated carbohydrates.

In Stefin B, the Gly-9 residue along with <scene name='Papain/~~Sk_inhibitor_6~~/3'>two hairpin loops</scene> form a "wedge" complementary to the active site groove of papain. This wedge makes extensive and tight interactions with papain and a total of 128 intermolecular atom-atom interactions occur. <scene name='Papain/Sk_inhibitor_1/1'>Residue segments</scene> Met6-Pro11, Gln53-Asn59, Gln101-His104 and Tyr-124 - Phe-125 on the wedge all have some interaction to the enzyme though not always direct. All residues from the base and both sides of the <scene name='Papain/Sk_inhibitor_2/1'>active site cleft</scene> are involved in the complex with the inhibtor (Trp-177, Ser-21, Cys-63, Cys-25, Asp-158 and His-159).

In Stefin B, the Gly-9 residue along with <scene name='Papain/Stf_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of papain. This wedge makes extensive and tight interactions with papain and a total of 128 intermolecular atom-atom interactions occur. <scene name='Papain/Sk_inhibitor_1/1'>Residue segments</scene> Met6-Pro11, Gln53-Asn59, Gln101-His104 and Tyr-124 - Phe-125 on the wedge all have some interaction to the enzyme though not always direct. All residues from the base and both sides of the <scene name='Papain/Sk_inhibitor_2/1'>active site cleft</scene> are involved in the complex with the inhibtor (Trp-177, Ser-21, Cys-63, Cys-25, Asp-158 and His-159).

There are a small number of <scene name='Papain/Sk_inhibitor_3/1'>direct hydrogen bonds</scene> between stefin B and papain, however there are many more polar interactions mediated by <scene name='Papain/Sk_inhibitor_4/3'>solvent bridges</scene>. Thirteen solvent molecules bridge polar residues of the enzyme and inhibitor. Seventeen hydrogen bonds are made with a solvent molecule and stefin. Fourteen of these bridges form a papain contact. The rest of the interactions are largely hydrophobic-- involving apolar <scene name='Papain/Sk_inhibitor_5/3'>Van der Waals interactions</scene>.<ref> PMID:2347312 </ref>

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@@ Line 53: / Line 53: @@
 ==='''Stefin B'''===
-<scene name='Papain/Sk_inhibitor_0/2'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases-- it binds tightly but reversibly to the papain active site.  Stefin inhibitors are characterized by M<sub>r</sub> of about 11,000, no disulfide bonds and no associated carbohydrates.
+<scene name='Papain/Stefin_b/1'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases- it binds tightly but reversibly to the papain active site.  Stefin inhibitors are characterized by M<sub>r</sub> of about 11,000, no disulfide bonds and no associated carbohydrates.
-In Stefin B, the Gly-9 residue along with <scene name='Papain/Sk_inhibitor_6/3'>two hairpin loops</scene> form a "wedge" complementary to the active site groove of papain.  This wedge makes extensive and tight interactions with papain and a total of 128 intermolecular atom-atom interactions occur.  <scene name='Papain/Sk_inhibitor_1/1'>Residue segments</scene> Met6-Pro11, Gln53-Asn59, Gln101-His104 and Tyr-124 - Phe-125 on the wedge all have some interaction to the enzyme though not always direct.  All residues from the base and both sides of the <scene name='Papain/Sk_inhibitor_2/1'>active site cleft</scene> are involved in the complex with the inhibtor (Trp-177, Ser-21, Cys-63, Cys-25, Asp-158 and His-159).
+In Stefin B, the Gly-9 residue along with <scene name='Papain/Stf_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of papain.  This wedge makes extensive and tight interactions with papain and a total of 128 intermolecular atom-atom interactions occur.  <scene name='Papain/Sk_inhibitor_1/1'>Residue segments</scene> Met6-Pro11, Gln53-Asn59, Gln101-His104 and Tyr-124 - Phe-125 on the wedge all have some interaction to the enzyme though not always direct.  All residues from the base and both sides of the <scene name='Papain/Sk_inhibitor_2/1'>active site cleft</scene> are involved in the complex with the inhibtor (Trp-177, Ser-21, Cys-63, Cys-25, Asp-158 and His-159).
 There are a small number of <scene name='Papain/Sk_inhibitor_3/1'>direct hydrogen bonds</scene> between stefin B and papain, however there are many more polar interactions mediated by <scene name='Papain/Sk_inhibitor_4/3'>solvent bridges</scene>.  Thirteen solvent molecules bridge polar residues of the enzyme and inhibitor.  Seventeen hydrogen bonds are made with a solvent molecule and stefin.  Fourteen of these bridges form a papain contact.  The rest of the interactions are largely hydrophobic-- involving apolar <scene name='Papain/Sk_inhibitor_5/3'>Van der Waals interactions</scene>.<ref> PMID:2347312 </ref>